Newbie question

Hello, would like to get some advice on a site I am currently working on. Is it better to embed a flash swf into a html page or have it posted on the site as a flash file. By this i mean that the initial or index page is in html to advise visitors that they must have the current Flashplayer installed on their system but would you advise that the other links be embedded into html pages or left alone as Flash files with their own html files.